John Tulloh. Egypt’s new would-be Pharaoh.

The headline in The Australian was stark and brutal: SISI VOWS TO ERADICATE BROTHERHOOD. Eradicate? This is a word you associate with efforts to get rid of a disease or an agricultural pest. But in this case it was meant as a kind of cleansing of religious adherents and caused barely a ripple of protest outsider Egypt.

The story, of course, referred to Egypt’s new strongman, Abdel Fattah al-Sisi, who has won this week’s presidential election. He says one of his first tasks will be to suppress the Moslem Brotherhood out of existence. His interim government has already declared it a terrorist group.

The Moslem Brotherhood has been an organisation long feared by Egypt’s leaders because of its shadowy presence like an underground movement and yet having enough support for effective political influence. It demonstrated that in 2011 when it won almost a majority of seats in parliament and in 2012 when its candidate, Mohamed Morsi, won the presidential election with 51% of the vote. This was a stunning result given that the Moslem Brotherhood had virtual illegal status for six decades.

All that came to an end last July when al-Sisi staged a military coup and ousted Morsi, who has been under arrest ever since. Huge protests in support of Morsi followed which the military ruthlessly put down. More than 600 people died, said to be the worst mass killing in modern Egyptian history.

The Moslem Brotherhood was founded in 1928. It favoured Sharia law and wanted Egypt to be governed according to the teachings of the Koran. Within 20 years it had an estimated two million members.

But it was long regarded as a pest to Egyptian authority. It has been accused over the decades of murders, assassinations, bombings, arson attacks and plots, which is why it has been for so long been treated as a threat from within. Yet it also has been associated with charity work in a country with endemic poverty.

Al-Sisi in an interview earlier this month said the Moslem Brotherhood was ‘finished’. Asked if it would cease to exist if he were elected president, he was quoted as saying ‘Yes, just like that’. Eradicated! Most of the Brotherhood’s political leadership has been imprisoned or fled the country. Any sign of support, real or imagined, is harshly dealt with as Australian journalist Peter Greste and two Al-Jazeera colleagues have discovered. They have been locked up for five months without a shred of evidence against them.

Many Egyptians are hoping al-Sisi can provide some welcome stability. Egypt has become a dystopia. The once booming tourist industry has collapsed because of unrest. The enormous bureaucracy still toils in a pre-computer era. Essential and social services are in disarray. Unemployment is rampant and the outlook is not only grim, but ripe for unrest.

According to the Egyptian author, Thanassis Cambanis, al-Sisi wants to restore Egypt’s standing as the most powerful country in the Arab world. He (al-Sisi) thinks only one institution can do this: the military. This recalls the 50s and 60s when another former army officer, Gamal Abdel Nasser, ruled the country and was the most powerful of all Arab leaders.

Cambanis, writing in Time magazine, says: ‘According to advisers who’ve heard his private comments, al-Sisi wants Egypt to project power in the region, rather than be seen as a basket case that can be manipulated by the oil sheikhs in the Gulf’.

If al-Sisi really does want Egypt to assert its former military muscle, he might have an opportunity beyond the country’s borders. Ethiopia is building a dam on the Blue Nile – part of Egypt’s lifeblood – and, if al-Sisi sees this as a threat to his citizens’ fresh water supply, he may see that as a just cause for military action.

What of the Moslem Brotherhood? Ashraf Khalil, a Cairo journalist and author, says if it has any hope of playing a future political role, ‘it needs to acknowledge – to itself and the rest of Egypt – that its downfall was partially its own fault. Through a combination of arrogance, incompetence and ham-fisted politics, Morsi and the Brotherhood managed to systematically alienate every potential ally they had’.

Whatever displeasure the West has felt at a democratically-elected government being overthrown has been muted. Under the Foreign Assistance Act, the U.S. is supposed to reduce or suspend aid to guilty regimes. But little has happened apart from delaying the delivery of some Apache helicopters. No doubt this is because Egypt can be counted on to curb terrorism and has been a steadfast supporter of Western interests, thanks in part to its military and economy relying so much on Washington’s aid.

In the months and years ahead, you can be sure that Egypt’s formidable security apparatus will be closely monitoring sermons in the mosques for any sign of dissent. As it is even today, the clerics are supposed to follow official government advice of what sermon topics are acceptable.